5ZZB

LokiProfilin2/Rabbit Actin Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Genomes of Asgard archaea encode profilins that regulate actin.

Akil, C.Robinson, R.C.

(2018) Nature 562: 439-443

  • DOI: 10.1038/s41586-018-0548-6
  • Primary Citation of Related Structures:  
    5YED, 5YEE, 5ZZA, 5ZZB

  • PubMed Abstract: 
  • The origin of the eukaryotic cell is unresolved 1,2 . Metagenomics sequencing has recently identified several potential eukaryotic gene homologues in Asgard archaea 3,4 , consistent with the hypothesis that the eukaryotic cell evolved from within the Archaea domain ...

    The origin of the eukaryotic cell is unresolved 1,2 . Metagenomics sequencing has recently identified several potential eukaryotic gene homologues in Asgard archaea 3,4 , consistent with the hypothesis that the eukaryotic cell evolved from within the Archaea domain. However, many of these eukaryotic-like sequences are highly divergent and the organisms have yet to be imaged or cultivated, which brings into question the extent to which these archaeal proteins represent functional equivalents of their eukaryotic counterparts. Here we show that Asgard archaea encode functional profilins and thereby establish that this archaeal superphylum has a regulated actin cytoskeleton, one of the hallmarks of the eukaryotic cell 5 . Loki profilin-1, Loki profilin-2 and Odin profilin adopt the typical profilin fold and are able to interact with rabbit actin-an interaction that involves proteins from species that diverged more than 1.2 billion years ago 6 . Biochemical experiments reveal that mammalian actin polymerizes in the presence of Asgard profilins; however, Loki, Odin and Heimdall profilins impede pointed-end elongation. These archaeal profilins also retard the spontaneous nucleation of actin filaments, an effect that is reduced in the presence of phospholipids. Asgard profilins do not interact with polyproline motifs and the profilin-polyproline interaction therefore probably evolved later in the Eukarya lineage. These results suggest that Asgard archaea possess a primordial, polar, profilin-regulated actin system, which may be localized to membranes owing to the sensitivity of Asgard profilins to phospholipids. Because Asgard archaea are also predicted to encode potential eukaryotic-like genes involved in membrane-trafficking and endocytosis 3,4 , imaging is now necessary to elucidate whether these organisms are capable of generating eukaryotic-like membrane dynamics that are regulated by actin, such as are observed in eukaryotic cell movement, podosomes and endocytosis.


    Organizational Affiliation

    Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan. rrobinson@imcb.a-star.edu.sg.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin, alpha skeletal muscleA [auth B],
C [auth D]
371Oryctolagus cuniculusMutation(s): 0 
Gene Names: ACTA1ACTA
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
Explore P68135 
Go to UniProtKB:  P68135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68135
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinB [auth A],
D [auth C]
136Lokiarchaeum sp. GC14_75Mutation(s): 0 
Gene Names: Lokiarch_27400
UniProt
Find proteins for A0A0F8XMN8 (Lokiarchaeum sp. (strain GC14_75))
Explore A0A0F8XMN8 
Go to UniProtKB:  A0A0F8XMN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F8XMN8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
F [auth B],
I [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
LAB
Query on LAB

Download Ideal Coordinates CCD File 
E [auth B],
H [auth D]
LATRUNCULIN B
C20 H29 N O5 S
NSHPHXHGRHSMIK-JRIKCGFMSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth B],
J [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.85α = 90
b = 123.3β = 96.9
c = 88.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.3: 2018-12-05
    Changes: Data collection, Database references